| 1 | Banner Intro |
| 2 | Title |
| 3 | Options |
| 4 | Opening |
| 5 | Prologue |
| 6 | Sector 1: Brilliant Garden |
| 7 | Expedition Complete |
| 8 | Select Sector |
| 9 | Inside the S.S. Dolphin II |
| 10 | Select Area (Sector 1) |
| 11 | Expedition Start |
| 12 | Sector 1: Brilliant Garden (Back Side) |
| 13 | Expedition Results |
| 14 | Pikmin Park |
| 15 | Pikmin Park Sparklium |
| 16 | Pikmin Park Treasure |
| 17 | Secret Spot Intro |
| 18 | Secret Spot |
| 19 | Secret Spot Clear |
| 20 | Secret Spot Failure |
| 21 | Secret Spot Olimar is Down |
| 22 | Secret Spot Results |
| 23 | Underground |
| 24 | Underground (Back Side) |
| 25 | Sparklium Springs Start |
| 26 | Sparklium Springs |
| 27 | Sparklium Springs End |
| 28 | Sparklium Springs Results |
| 29 | Inside the S.S. Dolphin II (Boss Found) |
| 30 | Boss Area |
| 31 | Red Bulborb Cutscene |
| 32 | VS. Red Bulborb |
| 33 | Boss Defeated |
| 34 | Select Area (Sector 2) |
| 35 | Sector 2: Verdant Waterfront |
| 36 | Sector 2: Verdant Waterfront (Back Side) |
| 37 | Olimar is Down |
| 38 | Game Over |
| 39 | Long Water Dumple Cutscene |
| 40 | VS. Long Water Dumple |
| 41 | Select Area (Sector 3) |
| 42 | Sector 3: Sparkling Labyrinth |
| 43 | Sector 3: Sparkling Labyrinth (Back Side) |
| 44 | Logs |
| 45 | Log Complete |
| 46 | Armurk Cutscene |
| 47 | VS. Armurk |
| 48 | Select Area (Sector 4) |
| 49 | Sector 4: Ravaged Rustworks |
| 50 | Sector 4: Ravaged Rustworks (Back Side) |
| 51 | Electric Cottonade Cutscene |
| 52 | VS. Electric Cottonade |
| 53 | Select Area (Sector 5) |
| 54 | Sector 5: Leafswirl Lagoon |
| 55 | Sector 5: Leafswirl Lagoon (Back Side) |
| 56 | Sector 5: Leafswirl Lagoon 2 |
| 57 | Sector 5: Leafswirl Lagoon 2 (Back Side) |
| 58 | Queen Shearwig Cutscene |
| 59 | VS. Queen Shearwig |
| 60 | Select Area (Sector 6) |
| 61 | Sector 6: Sweltering Parchlands |
| 62 | Sector 6: Sweltering Parchlands (Back Side) |
| 63 | Sizzling Precipice |
| 64 | Sizzling Precipice (Back Side) |
| 65 | Fiery Blowhog Cutscene |
| 66 | VS. Fiery Blowhog |
| 67 | Select Area (Sector 7) |
| 68 | Sector 7: Snowfall Field |
| 69 | Sector 7: Snowfall Field (Back Side) |
| 70 | Over Wintry Mountains |
| 71 | Luring Slurker Cutscene |
| 72 | VS. Luring Slurker |
| 73 | Select Area (Sector 8) |
| 74 | Sector 8: Lushlife Murk |
| 75 | Sector 8: Lushlife Murk (Back Side) |
| 76 | Olimar's Madcap Ride |
| 77 | Emperor Bulblax Cutscene |
| 78 | VS. Emperor Bulblax |
| 79 | Emperor Bulblax Defeated |
| 80 | Berserk Leech Hydroe (Buried Form) Cutscene |
| 81 | VS. Berserk Leech Hydroe (Buried Form) |
| 82 | Berserk Leech Hydroe (Quadruped Form) Cutscene |
| 83 | VS. Berserk Leech Hydroe (Quadruped Form) |
| 84 | Berserk Leech Hydroe (Winged Form) Cutscene |
| 85 | VS. Berserk Leech Hydroe (Winged Form) |
| 86 | Berserk Leech Hydroe Defeated |
| 87 | Epilogue |
| 88 | Ending |
| 89 | Staff Roll |
